Mapping and annotating genomic loci to prioritize genes and implicate distinct polygenic adaptations for skin color

Beomsu Kim, Dan Say Kim, Joong-Gon Shin, Sangseob Leem, Minyoung Cho, Hanji Kim, Ki-Nam Gu, Jung Yeon Seo, Seung Won You, Alicia R. Martin, Sun Gyoo Park, Yunkwan Kim, Choongwon Jeong, Nae Gyu Kang () and Hong-Hee Won ()
Additional contact information
Beomsu Kim: Samsung Medical Center
Dan Say Kim: Samsung Medical Center
Joong-Gon Shin: LG Household & Healthcare (LG H&H)
Sangseob Leem: LG Household & Healthcare (LG H&H)
Minyoung Cho: Samsung Medical Center
Hanji Kim: LG Household & Healthcare (LG H&H)
Ki-Nam Gu: LG Household & Healthcare (LG H&H)
Jung Yeon Seo: LG Household & Healthcare (LG H&H)
Seung Won You: LG Household & Healthcare (LG H&H)
Alicia R. Martin: Massachusetts General Hospital and Harvard Medical School
Sun Gyoo Park: LG Household & Healthcare (LG H&H)
Yunkwan Kim: LG Household & Healthcare (LG H&H)
Choongwon Jeong: Seoul National University
Nae Gyu Kang: LG Household & Healthcare (LG H&H)
Hong-Hee Won: Samsung Medical Center

Nature Communications, 2024, vol. 15, issue 1, 1-16

Abstract: Abstract Evidence for adaptation of human skin color to regional ultraviolet radiation suggests shared and distinct genetic variants across populations. However, skin color evolution and genetics in East Asians are understudied. We quantified skin color in 48,433 East Asians using image analysis and identified associated genetic variants and potential causal genes for skin color as well as their polygenic interplay with sun exposure. This genome-wide association study (GWAS) identified 12 known and 11 previously unreported loci and SNP-based heritability was 23–24%. Potential causal genes were determined through the identification of nonsynonymous variants, colocalization with gene expression in skin tissues, and expression levels in melanocytes. Genomic loci associated with pigmentation in East Asians substantially diverged from European populations, and we detected signatures of polygenic adaptation. This large GWAS for objectively quantified skin color in an East Asian population improves understanding of the genetic architecture and polygenic adaptation of skin color and prioritizes potential causal genes.

Date: 2024
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DOI: 10.1038/s41467-024-49031-4

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